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Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution – Share Alike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/ We have reviewed this material in accordance with U.S. Copyright Law and have tried to maximize your ability to use, share, and adapt it. The citation key on the following slide provides information about how you may share and adapt this material. Copyright holders of content included in this material should contact [email protected] with any questions, corrections, or clarification regarding the use of content. For more information about how to cite these materials visit http://open.umich.edu/education/about/terms-of-use. Any medical information in this material is intended to inform and educate and is not a tool for self-diagnosis or a replacement for medical evaluation, advice, diagnosis or treatment by a healthcare professional. 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To use this content you should do your own independent analysis to determine whether or not your use will be Fair. M1 Renal: Nitrogen Metabolism (and Related Topics) • Amino Acid Metabolism (Nitrogen metabolism) • Folate Metabolism (“One-Carbon pathways”) • Nucleotide Metabolism Dr. Robert Lyons Assistant Professor, Biological Chemistry Director, DNA Sequencing Core Web: http://seqcore.brcf.med.umich.edu/mcb500 Fall 2008 R. Lyons Supplementary study material on the Web: http://seqcore.brcf.med.umich.edu/mcb500 Amino Acid met abolism A mino acids Folat e met abolism Met hylene THF Glu, Gln, Asp , NH3 Met Cycle Urea oxaloac et at e Pu r in e s Uric Acid DNA RNA Py r im id in e s ( energy ) f um arat e TCA Cycle R. Lyons Nucleic Acid met abolism Protein Degradation: • Endogenous proteins degrade continuously - Damaged - Mis-folded - Un-needed • Dietary protein intake - mostly degraded Nitrogen Balance - expresses the patient’s current status - are they gaining or losing net Nitrogen? Transaminases Collect Amines General react ion overview: H H R1 C COO NH2 amino acid (-) (-) + R1 C O R2 C COO O -keto acid (typically alpha-ketoglutarate) COO (-) + R2 C COO (-) NH2 amino acid (typically glutamate) -keto acid Det ails of react ion mechanism: -keto acid amino acid H R C (-) COO NH2 + O CH P OCH2 N CH3 H pyridoxal phosphate R. Lyons R C (-) COO R C N CH OH + H+ H H2 O P OCH2 + N H OH CH3 P OCH2 (-) COO R C N N CH HCH OH N CH3 H P OCH2 + N H (-) COO OH CH3 (-) R C COO O + NH2 HCH P OCH2 OH CH3 N H pyridoxamine phosphate + Transfer the amine back to an acceptor -keto acid NH2 O CH HCH P OCH2 OH + N CH3 H pyridoxamine phosphate R. Lyons + R C O (-) COO -keto acid P OCH2 H OH + N CH3 H pyridoxal phosphate + R C COO NH2 amino acid In peripheral tissues, transaminases tend to form Glutamate when they catabolize amino acids In other words, alpha-ketoglutarate is the preferred acceptor, and Glutamate is the resulting amino acid: Some amino acid + -ketoglutarate some alpha keto acid + Glutamate Glutamate can donate its amines to form other amino acids as needed A specific example - production of Aspartate in liver (described a few slides from now): Glutamate + oxaloacetate -ketoglutarate + aspartate Ge t t ing A m ine s Int o t he Liv e r Glutamate Dehydrogenase: H (-) O2C CH2CH2C CO(-) 2 NAD(P) O2C CH2CH2C CO(-) 2 (-) (mito) NH2 glutamate NAD(P)H Glutamine Synthetase: OOC C -ketoglutarate (-) (-) OOC CH2CH2 COO (+) glut amat e R. Lyons ammonia H NH3 ATP+ NH3 NH3 O H (- ) + ADP+ Pi C O CH2CH2C NH3 (+ ) glut amine NH2 . In t he Liv e r: Pre curse rs f or Ure a Cy cle Glut amine is hydrolyzed t o glut amat e and ammonia: H (-) OOC H O C CH2CH2C NH3 (-) O OC NH2 (+) CH2CH2 C N H3 H2O glut amine O C OH (+) NH3 glut amat e Ammonia can also be formed by the glutamate dehydrogenase reaction and several other reactions as well. Glut amat e donat es it s amino group t o f orm aspart at e: Glut amat e-aspartat e aminot ransferase: H (- ) O 2C CH2 CH2 C H CO(-) 2 N H2 Glutamate . R. Lyons + ( -) O 2CC H2 C H CO(2-) O oxaloacetate (- ) O 2C CH2 CH2 C C O(-) 2 O -keto glutarate + (- ) O 2C CH 2 C CO(-) 2 NH2 aspartate 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e Carb am o y l p h o s p h at e sy n t h e t as e I NH ATP O HO C ATP 3 (- ) HO O b ic ar b on at e R. Lyons C O P HO c ar bo ny l ADP ph os p ha te O O O Pi C P O NH 2 ca rb a ma te C NH 2 ca rb a mo yl ADP ph os p ha te O r n it h in e T r a n s c a r b a m o y la s e Carb am o y l p ho s p hat e O N H2 C Pi ( -) O P O3 H ( -) OO C (+ ) C H C H2 C H2 N H 3 2 C NH (+ ) 3 O r n it h in e R. Lyons (- ) OOC H O C C H 2C H2 C H2 N H C NH (+ ) 3 C it r u llin e NH 2 A r g in in o s u c c in a t e s y n t h e t a s e H (-) O2CC 2C CO2(-) H NH2 aspartate H (-) OOC C NH (+) 3 H O CH2CH2CH2NH C NH2 (-) OOC (+) CH2CH2CH2NH C NH2 NH3 Cit rulline (+) ATP R. Lyons C H (-) O2CCH2C CO(-) 2 NH2 AMP + PPi A rgininosuccinat e A r g in in o s u c c in a t e ly a s e H (-) O2CCH2C CO2 NH2 (-) H (-) OOC C H (-) (+) CH2CH2CH2NH C NH2 OOC C NH3 (+) (+) Argininosuccinat e H (-) O2C C C CO2 H (-) Fumarat e R. Lyons CH2CH2CH2NH C NH2 NH NH3 (+) 2 A rginine A r g in a s e H H (-) OOC (-) OOC C CH2CH2CH2NH C NH2 NH NH3 (+) 2 H2 O O NH2 C NH2 Urea R. Lyons CH2CH2CH2NH(+) 3 NH (+) 3 (+) Arginine C Ornit hine 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e Urea Cycle Connect s t o TCA Cycle H (-) O2CCH2C CO(-) 2 Ornithine NH2 Citrulline Aspartate Urea Urea Cycle Arginine Argininosuccinate Oxaloacetate Malate H O2C C C CO(-) 2 H (-) Fumarate TCA Cycle -Ketoglutarate R. Lyons Citrate Ge t t ing A m ine s Int o t he Liv e r Glutamate Dehydrogenase: H (-) O2C CH2CH2C CO(-) 2 NAD(P) O2C CH2CH2C CO(-) 2 (-) (mito) NH2 glutamate NAD(P)H Glutamine Synthetase: OOC C -ketoglutarate (-) (-) OOC CH2CH2 COO (+) glut amat e R. Lyons ammonia H NH3 ATP+ NH3 NH3 O H (- ) + ADP+ Pi C O CH2CH2C NH3 (+ ) glut amine NH2 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e C P S I is S t im u la t e d b y N A G H O (-) N -a c e t y l H O (-) OOC OOC CH CH C C 2 + 2 N H3 g lu t a m a t e Co A - C OH O C CH CH C 2 2 OH NH s y n t h e t as e C C H3 ( +) O C H3 g lu t a m a t e N - a c e t y l g lu t a m a t e a c e t y l Co A ( N A G) ( r e p e a t in g t h e f ig u r e f r o m p a g e 3 o f y o u r h an d o u t ) NH ATP O HO C ( -) bi ca rb o na te R. Lyons HO O C ATP 3 O O P HO c a rb on y l ADP p ho s ph at e O O Pi C P O NH 2 c ar ba m at e C NH 2 c ar ba m oy l ADP p ho sp h at e -Muscle (Amines) Glucose Pyruvate Glutamate Amino acids -ketoglutarate Alanine blood transport Alanine -ketoglutarate Glucose Glutamate Pyruvate Live r R. Lyons Urea NH3 Complicating the picture: Other tissues may be involved Muscle: Amino acids: Transamination Deamination Alanine purine deamination: (+) Glutamate NH4 Glutamine Intestine: Glutamine (+) Alanine NH4 Glutamine Citrulline Kidney: Citrulline NH3 (+) NH4 Arginine Liver: Arginine Glutamine (+) NH4 Alanine Glu R. Lyons Aspartate Urea Why is Ammonia Toxic? Why is Ammonia Toxic? • Possible neurotoxic effects on glutamate levels (and also GABA) (due to shifting equilibria of reactions involving these compounds) Why is Ammonia Toxic? • Possible neurotoxic effects on glutamate levels (and also GABA) (due to shifting equilibria of reactions involving these compounds) • Possible metabolic/energetics effects: - alpha-ketoglutarate levels - glutamate levels - glutamine 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e Inherited Defects of Urea Cycle Enzymes: Diagnosis Defects are diagnosed based on the metabolites seen in the blood and/or urine. CPSD OTCD ASD ALD AD No elevation except ammonia; diagnosed by elimination. Elevated CP causes synthesis of Orotate Elevated citrulline Elevated argininosuccinate Elevated arginine 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e C P S I is S t im u la t e d b y N A G H O (-) N -a c e t y l H O (-) OOC OOC CH CH C C 2 + 2 N H3 g lu t a m a t e Co A - C OH O C CH CH C 2 2 OH NH s y n t h e t as e C C H3 ( +) O C H3 g lu t a m a t e N - a c e t y l g lu t a m a t e a c e t y l Co A ( N A G) ( r e p e a t in g t h e f ig u r e f r o m p a g e 3 o f y o u r h an d o u t ) NH ATP O HO C ( -) bi ca rb o na te R. Lyons HO O C ATP 3 O O P HO c a rb on y l ADP p ho s ph at e O O Pi C P O NH 2 c ar ba m at e C NH 2 c ar ba m oy l ADP p ho sp h at e 2ATP + HCO3 + NH3 Carbamoy l phosphat e O (-) NH2 C OPO3 1 Pi 2 2ADP + Pi H (-) OOC C H (+) (-) CH2CH2CH2NH3 OOC NH3 O CH2CH2 CH2NH C NH2 C NH (+) 3 (+) Ornit hine Cit rulline Liver mitochondrion Liver cyt oplasm H H (-) OOC (-) OOC CH2CH2CH2NH(+) 3 C NH NH3 (+) O CH2CH2CH2NH C NH2 C (+) 3 Cit rulline Ornit hine O NH2 C NH2 H O2CCH2 C CO(-) 2 NH2 aspartate ATP (-) Urea 3 5 AMP + PPi H2O H H O2CCH2C CO(-) 2 NH2 C CH2CH2CH2NH C NH(+) 2 H (-) OOC (-) C CH2CH2CH2NH C NH2 NH2 NH3 (+) (-) OOC (+) NH3 A rginine (+) 4 H (-) O2C C C CO2 H (-) Fumarat e R. Lyons A rgininosuccinat e Clinical Management of Urea Cycle Defects • Dialysis to remove ammonia • Provide the patient with alternative ways to excrete nitrogenous compounds: * Intravenous sodium benzoate or phenylacetate * Supplemental arginine carbamoyl phosphate Excreted by kidney Ornithine O NH2 C NH2 Citrulline ATP Urea AMP+PP i HO 2 Arginine Aspartate XASD Argininosuccinate Excreted by kidney XALD Dietary Arginine R. Lyons • Levulose - acidifies the gut • Low protein diet Degrading the Amino Acid Carbon Backbone Easily-degraded products after transamination: H (-) O2C CH2C CO(-) 2 NH3 (+) aspartate (-) t ransaminat ion O2CCH2C CO(-) 2 O oxaloacetate H (-) O2C CH2CH2C CO2 NH (+) 3 glutamate (-) (-) (-) t ransaminat ion O2C CH2CH2C CO2 O -ketoglutarate t ransaminat ion CH3 C CO(-) 2 O pyruvate H (-) CH3 C CO2 NH3 (+) alanine R. Lyons We also already know how to degrade Glutamine: glutaminase Glutamine ----------------> glutamate + ammonia …and by analogy, how to degrade Asparagine: asparaginase Asparagine ---------------> aspartate + ammonia Amino Acids are categorized as ‘Glucogenic’ or ‘ketogenic’ or both. Many amino acids are purely glucogenic: Glutamate, aspartate, alanine, glutamine, asparagine,… Some amino acids are both gluco- and ketogenic: Threonine, isoleucine, phenylalanine, tyrosine, tryptophan The only PURELY ketogenic Amino Acids: leucine, lysine H (-) OOC C CH2CH2CH2NH C NH2 NH2 NH3 (+) (+) Arginine Urea ( via t he urea cy cle) H (-) OOC C CH2CH2CH2NH(+) 3 NH Amino acids with 5-carbon backbones tend to form -ketoglutarate (+) 3 Ornit hine -ket oglut arat e glut amat e H (-) OOC C (-) O CH2CH2C NH3 OOC H (+) N H Proline (+) glut amat e - 5 - semialdehyde (+) NAD(P) NA D(P)H H (-) OOC C H O CH2CH2C NH3 (-) OOC OH - ket oglut arat e R. Lyons O CH2CH2C NH3 (+) glut amat e C (+) NH3 H2O glut amine NH2 Degradation and Biosynthesis of Serine and Glycine (+) NADH NAD H (-) OOC C Glycine Synthase: NH3 CO2 (+) (+) NH4 + H THF Glycine (-) Serine Hydroxymethyltransferase: OOC CH N5 -N10- methylene THF (-) OOC NH3 (+) CH2OH THF Serine N5 -N10- methylene THF C H 2 Gly cine H 2O Serine Dehydratase: (-) OOC CH NH (+)3 CH2OH Serine R. Lyons NH (+) 3 (+) NH4 (-) OOC C CH2 (+) NH3 (-) OOC C CH3 (+) (-) NH2 OOC H 2O C CH3 O H H CH3 S CH2 CH3 (-) CH2 C COO CH2 S CH2 C CH2 NH3 (+) (+) ATP + HO 2 NH (+) 3 O PPi + Pi (-) COO H H Ad en in e H H OH OH Met hionine S-A denosyl Met hionine Met h yl a cce pt o r te t rah yd ro fo lat e Bi os ynt h et ic Me t hy lat io n re act io n * se e e xam pl es N5 me th yl t et rah yd ro fo la te Methionine Cycle And Biological Methyl Groups Me t hyl at ed acc ep to r H (+) H HS CH2 CH2 C (-) NH3 H NH Ad en in e S-Adenosy l Homoc yst eine (-) CH2 C COO NH3 (+) Serine H CH2 C (-) COO NH (+) 3 Cy st eine (remainder of homocysteine degraded for energy) H H H OH OH Homoc yst eine HS (-) COO (+) 3 O (+) HO CH2 C CH2 COO H R. Lyons CH2 HS Phenylalanine and Tyrosine (Normal pat h shown in black, pat hological react ion shown in red) Tetrahydrobiopterin + O2 Dihydrobiopterin + H2O (+) NH 3 CH2 CH (-) (-) COO Phenylpyruvat e CH (-) COO Tyrosine Homogent isat e O R. Lyons CH2 Enzyme: Phenylalanine hydroxylase Phenylket onuria (no phenylalanine hydroxylase) C NH 3 HO COO Phenylalanine CH2 (+) Deficiency: Alkaptonuria “Ochronosis” Enz yme: homogent isat e dioxy genase (you don’ t need t o know t he rest ) Branched Chain Amino Acids Isoleucine CH3 CH2 CH CH CH3 Leucine (-) COO CH3CH CH 2 NH3 CH3 (+) CH Valine (-) COO NH3 CH3 CH (-) COO CH3 NH3 (+) (+ ) -KG -KG CH -KG --- ------------ - Transaminat ion -------- -------Glu CH3 CH2 CH C CH3 Glu (-) COO O CH3CHCH 2 C CH3 O + (-) COO Glu CH3CH C CH3 O NAD,+ CoASH NAD,+ CoASH NAD, CoASH (-) COO --- Branched-chain -ket o acid dehydrogenase - -NADH + CO CH3 CH2 CH CH3 C O S-CoA NADH + CO2 NADH + CO2 2 CH3CHCH 2 C CH3 O S-CoA CH3CH C S-CoA CH3 O ( cont inues on t o degradat ion pat h similar t o -oxidat ion of fatt y acids) R. Lyons Synt hesis of Bioact ive Amines (+) NH 3 HO CH 2 CH (-) COO NH 3 HO CH 2 Tyrosine hydroxy lase Tyrosin e HO HO (+) HO (+) HO CH 2CH 2NH 3 HO R. Lyons COO Dih ydroxyp heny lalanin e ( L-DOPA) OH HO (+) CH CH 2NH 3 H Dop am ine (-) CH No repine phrine HO OH CHCH 2 N CH 3 H H Ep ineph rine Synthesis of Bioactive Amines CH 2 N CH NH3 (+) Tryp t o ph an (-) HO COO Tryptophan hy droxylase CH2 N (-) COO NH (+) 3 5 -hyd roxyt ryp t o ph an PLP-de pe ndent de cvarboxylat ion CO2 HO CH 2 NAD+ N Sero t o nin R. Lyons CH CH2 NH3 (+) Synthesis of Bioactive Amines (-) (-) COO CH 2 CH2 CH COO NH3 (+) Glut amat e N N H CH2 NH (+) 3 Hist idine R. Lyons CH (-) Glutam ate de carboxylase ( PLP-depe ndent ) NH3 COO CH 2 CH 2 CH2 (+) -amin ob ut yric acid (GABA) N (COO) Hist idine de carboxylase ( PLP-de pe ndent ) N H CH2 CH2 Hist amine NH3 (+) NON-Essential Amino Acids: Glutamate, aspartate, alanine, glutamine, asparagine, (proline), glycine, serine (cysteine, tyrosine) Essential Amino Acids: Arginine (!), phenylalanine, methionine, histidine, Isoleucine, leucine, valine, threonine, tryptophan, lysine Additional Source Information for more information see: http://open.umich.edu/wiki/CitationPolicy Slide 4: Robert Lyons Slide 5: Robert Lyons Slide 7: Robert Lyons Slide 8: Robert Lyons Slide 11: Robert Lyons Slide 12: Robert Lyons Slide 13: Robert Lyons Slide 14: Robert Lyons Slide 15: Robert Lyons Slide 16: Robert Lyons Slide 17: Robert Lyons Slide 18: Robert Lyons Slide 19: Robert Lyons Slide 20: Robert Lyons Slide 21: Robert Lyons Slide 22: Robert Lyons Slide 23: Robert Lyons Slide 24: Robert Lyons Slide 25: Robert Lyons Slide 29: Robert Lyons Slide 31: Robert Lyons Slide 32: Robert Lyons Slide 33: Robert Lyons Slide 34: Robert Lyons Slide 36: Robert Lyons Slide 38: Robert Lyons Slide 39: Robert Lyons Slide 40: Robert Lyons Slide 41: Robert Lyons Slide 44: Robert Lyons Slide 45: Robert Lyons